Rob,
With 500+ river miles and lots of hours riding on a pontoon, I'll offer up my 2 cents.
Pontoon pros:
* In moving water, pontoons are great and very stable.
* Pontoons hold a ton of stuff and are pretty light.
* Durable and allow you to bounce off of rocks.
* Pretty easy to patch / repair.
Pontoon cons:
* Suck in the wind
* Awkward to move and load as a single person.
* If you don't have a pick up or utility trailer, set up and tear down will make you not want to use it.
* Hit a submerged stick, root ball or hunk of metal.....POP
* Check PFBC regulations, may need to register if motor is used.
Getting a boat for the sake of having one is probably not the best idea. Look at weight capacity be it a pontoon or kayak.
The boat you listed (Colorado) is OK and probably won't give you more than 2 seasons of use due to the build quality. Spend $500 and it may last 18-24 months versus investing $1000 that will last as long as you want it to. I think I got my boat for $900 plus shipping and it's at least 6 years old. It has at least 10 more years in it and I used it HARD.
You may be better served holding off and putting away a little more cash. Maybe you luck into a great deal, find a boat on sale, etc.
You also have to consider how much water you will cover and do you like rowing? Will you fish from the boat or use it as transportation to get from "A" to "B"? Kayaks are a good option for getting somewhere fast and the wide fishing models are pretty stable for fishing out of. Below is boat from swap forum that is a good deal. May not be exactly what you're looking for but it's bulletproof. Also consider FishCat 9' model as an alternative to the Colorado. The FishCat IR9 is a bit more but I've seen them on clearance recently. Next step up is something like a NFO Skykomish which I believe Cabelas still carries for right around $1000. Allows you to drop anchor and stand. Aluminum frame so, no rust. I don't want to see you drop $500 to turn around and like it resulting in you dropping another $1000+ in less than a year.
http://www.paflyfish.com/forums/Open-Forums/Swap-Forum/Water-Master-Grizzly-Raft-Package/14,36359.html
http://harrisburg.craigslist.org/search/sss?sort=date&query=kayak
http://lancaster.craigslist.org/search/sss?sort=date&query=kayak
http://www.cabelas.com/product/Emotion-Muskie-Angler-ft-Kayak/2202577.uts?productVariantId=4542185&srccode=cii_17588969&cpncode=40-134767339-2&WT.tsrc=CSE&WT.mc_id=GoogleProductAds&WT.z_mc_id1=04403968&rid=20